Pseudo-Chromosomal Genome Assembly in Combination with Comprehensive Transcriptome Analysis in Agaricus bisporus Strain KMCC00540 Reveals Mechanical Stimulus Responsive Genes Associated with Browning Effect

Abstract

Agaricus bisporus is one of the world’s most popular edible mushrooms, including in South Korea. We performed de novo genome assembly with a South Korean white-colored cultivar of A. bisporus, KMCC00540. After generating a scaffold-level genomic sequence, we inferred chromosome-level assembly by genomic synteny analysis with the representative A. bisporus strains H97 and H39. The KMCC00540 genome had 13 pseudochromosomes comprising 33,030,236 bp mostly covering both strains. A comparative genomic analysis with cultivar H97 indicated that most genomic regions and annotated proteins were shared (over 90%), ensuring that our cultivar could be used as a representative genome. However, A. bisporus suffers from browning even from only a slight mechanical stimulus during transportation, which significantly lowers its commercial value. To identify which genes respond to a mechanical stimulus that induces browning, we performed a time-course transcriptome analysis based on the de novo assembled genome. Mechanical stimulus induces up-regulation in long fatty acid ligase activity-related genes, as well as melanin biosynthesis genes, especially at early time points. In summary, we assembled the chromosome-level genomic information on a Korean strain of A. bisporus and identified which genes respond to a mechanical stimulus, which provided key hints for improving the post-harvest biological control of A. bisporus.

Screening of Lactiplantibacillus plantarum NML21 and Its Maintenance on Postharvest Quality of Agaricus bisporus through Anti-Browning and Mitigation of Oxidative Damage

“…During postharvest storage and transportation, the cellular integrity of A. bisporus is disrupted by oxidative stress or external factors. The cellular contents (polyphenols and PPO) react with oxygen and further undergo a browning reaction, resulting in pigment accumulation [ 27 ]. At present, controlling browning in white mushrooms is mainly based on reducing tissue cell breakage or inhibiting PPO activity, but this approach only delays the appearance of the pigment and does not effectively reduce the final browning extent [ 28 ].…”

“…The content of MDA was determined using the thiobarbituric acid method [ 27 ]. A total of 0.2 g of mushroom sample was ground in liquid nitrogen, and then 1.5 mL of 100 g L −1 trichloroacetic acid solution was added and mixed thoroughly.…”

Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus,Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling

“…The new C. cinerea genome eliminates several problems associated with previous annotated genomes of this species and Agaricomycetes in general. First, most Agaricomycete genomes are drafts and only a few are chromosome level assemblies (5)(6)(7)(8)(9)(10)(11), which limits their usefulness for downstream analyses. In addition, gene annotation is usually based on short-read assisted automatic pipelines, which fail to capture key gene features (e.g., APA, uORFs, UTRs) and often yield imprecise gene models; and thus incorrect or incomplete protein predictions due to challenges posed by overlapping gene models, polycistronic transcription (15,16), or microexons, among others.…”

“…This stems from the large diversity of basidiomycete model systems (4), the lack of systematic gene deletion projects, and the difficulty of extrapolating gene function from well-researched organisms, such as Saccharomyces cerevisiae, simply based on homology. Recent efforts have culminated in the publication of several chromosome-level assemblies of various Agaricomycetes (5)(6)(7)(8)(9)(10)(11). While these genomes represent a significant step in understanding the biology of these organisms, improvements of gene annotations did not follow that of contiguity.…”

Effect of Pleurotus eryngii on the Characteristics of Pork Patties during Freezing and Thawing Cycles

“…Compared to the control, patties with 0.50% Pe had significantly lower POV simultaneously (p < 0.05). During F-T cycles, the mechanical injury induced by mixing the meat caused the production of reactive oxygen species (ROS) and promoted the Millard reaction and lipid peroxidation, thence inducing a non-enzymatic browning reaction [48,49]. Similarly, mushrooms added to pork patties led to pro-oxidation immediately, thus promoting the volatile compounds to burst [11].…”